Egg-To-Fry Survival Of Chinook Salmon Studied In Several Columbia Basin Rivers, Provides Predictive Models For Researchers

A recent study brings to light the dangers of a little-known life stage in which spring Chinook salmon in the Columbia River basin generally incur high mortality – incubation in the gravel.

The study of spawning areas in several rivers that flow out of the east side of the Cascade Mountains quantifies impacts of substrate scour, scour depth and fine sediment accumulation on embryo survival, which one study author says can be difficult to effectively measure.

The study also provides predictive models that other researchers and fisheries managers can use to make their own estimates of Chinook salmon egg-to-fry survival, regardless of location, as the information is transferrable to other Columbia basin streams and spawning grounds.

“This information can be used to estimate the magnitude of loss relative to subsequent life-stages, to identify factors critical to incubation survival within a watershed, and to provide context for survival estimates relative to other upper and middle Columbia systems,” said Christopher Johnson, one of the study authors from the Washington Department of Fish and Wildlife and the School of Aquatic and Fisheries Sciences at the University of Washington, Seattle. “It is our hope that the findings can be used to not only determine if incubation survival is a concern, but also to inform and target habitat actions aimed at reducing embryo mortality.”

He said that the study highlights the variability in survival in time and space (over years, river basins and individual spawning sites), including areas very close to each other.

“Noteworthy is the magnitude of within-site variability in survival attributable to scour and/or fine sediment infiltration observed among redds in near proximity to one another,” Johnson said. “This finding emphasizes the importance of appropriate spatial scale when assessing incubation survival, and further highlights the remarkable plasticity of anadromous salmonids in selecting suitable areas for spawning.”

The environmental factors that negatively impact survival are high fines, flow-related scour, dewatering, high temperature and redd superimposition, the study says. As the basin warms, the authors say they would expect an increase in the influence of each of these variables, likely lowering survival of “these already stressed and depleted populations.”

“Many Columbia River salmonid populations are in danger of extinction, and we feel it important to note that documented trends of global scale warming may sizably affect the quality and availability of incubation habitats,” Johnson said. “Although many of the implications of such changes are outside the control of salmon managers, relationships such as those provided in this study will be essential to the identification of areas most at-risk for decreasing productivity, such that implemented habitat actions might moderate such effects.”

The study, “Factors affecting the survival of Chinook salmon (Oncorhynchus tshawytscha) embryos in upper and middle Columbia River watersheds,” was published Feb. 25 in the Canadian Journal of Fisheries and Aquatic Sciences (https://doi.org/10.1139/cjfas-2024-0250).

Authors are Johnson; Philip Roni, Cramer Fish Sciences in Issaquah, WA; Trenton De Boer, Yakama Nation Fisheries, Toppenish, WA; Andrew R. Murdoch, WDFW; and Thomas P. Quinn, U of W, School of Aquatic and Fishery Sciences, Seattle.

The researchers measured egg-to-fry survival in the Methow, Entiat, Wenatchee and Yakima river basins, all located on the east slope of the Cascades in Washington. The study area covered some 380 river kilometers (236 miles) of Chinook spawning habitat.

It was a long-term study. The researchers conducted four basin-scale studies of Chinook salmon egg-to-fry survival between 2009 and 2021 in the Columbia River tributaries; each study populations being currently supplemented or have a recent history of supplementation, and most listed under the federal Endangered Species Act, the study says.

“We detected a 16.8% decrease in the odds of survival for every 1-cm increase in substrate scour, a 1.0% decrease in the survival odds with each one-unit change in the percentage of accumulated fines, distinct differences in survival within and among rivers (from 30.5% to 82.5%), and subtle effects of parentage in the presence of environmental factors,” the study says. “The causal and predictive relationships provided here will inform conservation, restoration, and further research.”

Chinook salmon, due mostly to their size, have some advantages, according to the study. As the largest of Pacific salmon species, they can select spawning habitats across a wide range of stream depths and flows. And their larger size allows them to build deeper redds in coarser gravels, deeper water and in higher velocity flows, likely resulting in a lower probability of mortality due to scour. Still, egg-to-fry survival differed substantially among the rivers and study sites.

“Observed survival variability was largely explained by the magnitude of scour and fine sediment infiltration over the period of incubation, environmental metrics that varied at multiple scales across our study,” the study says.

How can salmon managers affect change? Johnson said the key is first to understand the system by “leveraging available data and perhaps investing in relevant data where it does not currently exist.”

Fisheries managers already document the location of Chinook redds every year, he said. Small studies that either model or collect data about the frequency and size of substrate scour and fine sediment accumulation are sufficient to make comparisons to other Columbia River systems.

“Managers may find that embryo survival is not a large concern at which point they can focus on other life-stage specific sources of mortality,” Johnson said. “Alternatively, if there are indications that incubation survival is a concern, the models provided can help managers focus recovery efforts locally to minimize impacts.”

Managers could modify policy and practices in areas of a watershed where the probability of egg-to-fry mortality is high, or take restoration actions such as riparian and floodplain restoration that could moderate substrate scour and the mobility of fine sediment.

Johnson said that the study authors also relied on “dedicated and enthusiastic people from a variety of state, federal, tribal, and non-governmental organizations, and from the community at-large. We are endlessly grateful to have had their support.”

For background, see:

— CBB, May 6, 2016, Field Based Salmon Egg-To-Fry Study In Upper Yakima System Shows Good Survival, Analyzes Factors, https://columbiabasinbulletin.org/field-based-salmon-egg-to-fry-study-in-upper-yakima-system-shows-good-survival-analyzes-factors/